COMPOSITIONS AND METHODS FOR DETECTING HEV NUCLEIC ACID

1 . A combination of oligomers for determining the presence or absence of hepatitis E virus (HEV) in a sample, said oligomer combination comprising at least three amplification oligomers and at least one detection probe oligomer, wherein:

the oligomer combinations are selected from the group consisting of

(a) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target hybridizing sequence consisting of SEQ ID NO:46 and a further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:37;

(b) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:37;

(c) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:67;

(d) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target hybridizing sequence consisting of SEQ ID NO:71;

(e) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:67;

(f) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:71;

(g) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:37;

(h) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:67;

(i) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:71;

(j) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a third amplification oligomer comprising a target hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:37;

(k) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a third amplification oligomer comprising a target hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:67; and

(1) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a third amplification oligomer comprising a target hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:71.

2 . The combination of oligomers of claim 1 , wherein the third amplification oligomer of (a), (e), (f), (g), (h), (i), (j), (k) and/or (1) comprises a nucleotide sequence consisting of SEQ ID NO:15.

3 . The combination of oligomers of claim 1 , wherein the third amplification oligomer of (b), (c), and/or (d) comprises a nucleotide sequence consisting of SEQ ID NO: 12.

4 . The combination of oligomers of claim 1 , wherein the second amplification oligomer of (g), (h), (i), (j), (k) and/or (1) comprises a nucleotide sequence of SEQ ID NO: 12.

5 . The combination of oligomers of claim 1 , wherein the combination comprises three detectably labeled detection probe oligomers, wherein (a), (b), (g), and (j) each further comprises a second detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:67 and a third detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:71.

6 . The combination of claim 1 , wherein the detectable label is an acridinium ester compound.

7 . A combination of oligomers, wherein the oligomer combination comprises at least four amplification oligomers and at least one detection probe oligomer, wherein:

the oligomer combination is selected from the group consisting of

(a) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a fourth amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:29 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:37;

(b) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a fourth amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:67;

(c) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, a fourth amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:29 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a detectably labeled detection probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:71.

8 . The combination of oligomers of claim 7 , wherein the combination comprises at least two detectably labeled detection probe oligomers, wherein the at least two detection probe oligomers comprise

(i) a first detectably labeled detection probe oligomer comprising the target-hybridizing sequence consisting of SEQ ID NO:37 and a second detectably labeled detection probe oligomer consisting of the target-hybridizing sequence consisting of SEQ ID NO:67, or

(ii) a first detectably labeled detection probe oligomer comprising the target-hybridizing sequence consisting of SEQ ID NO:37 and a second detectably labeled detection probe oligomer consisting of the target-hybridizing sequence consisting of SEQ ID NO:71.

9 . The combination of oligomers of claim 7 , wherein the third amplification oligomer promoter sequence and/or the fourth amplification oligomer promoter sequence consists of the sequence of SEQ ID NO:73.

10 . A kit comprising the combination of oligomers of claim 1 and at least one reagent suitable for performing an in vitro nucleic acid amplification reaction.

11 . The kit according to claim 10 , wherein the kit comprises an RNA polymerase.

12 . A kit comprising the combination of oligomers of claim 7 and at least one reagent suitable for performing an in vitro nucleic acid amplification reaction.

13 . The kit according to claim 12 , wherein the kit comprises an RNA polymerase.

14 . An amplification reaction mixture comprising the combination of oligomers of claim 1 .

15 . An amplification reaction mixture comprising the combination of oligomers of claim 7 .

16 . A method for determining the presence or absence of hepatitis E virus (HEV) in a sample, said method comprising:

(1) contacting a sample, said sample suspected of containing HEV, with at least three amplification oligomers for amplifying a target region of an HEV target nucleic acid, said amplification oligomer combination selected from the group consisting of

(a) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, and a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence;

(b) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, and a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence;

(c) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, and a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence;

(d) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, and a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence;

(e) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence;

(f) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:29, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence;

(g) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence; and

(h) a first amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:32, a second amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:24 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence, and a third amplification oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:46 and further comprising a promoter sequence joined to the 5′ end of the target-hybridizing sequence;

(2) performing an in vitro nucleic acid amplification reaction, wherein any HEV target nucleic acid present in the sample is used as a template for generating an amplification product; and

(3) detecting the presence or absence of the amplification product by using at least one detectably labeled detection probe oligomer selected from the group consisting of SEQ ID NO:37, SEQ ID NO:67, and SEQ ID NO:71, thereby determining the presence or absence of HEV in the sample.

17 . The method of claim 16 , wherein the third amplification oligomer of (a), (d), (e), (f), (g), and/or (h) comprises a nucleotide sequence consisting of SEQ ID NO: 15, and/or wherein the third amplification oligomer of (b) and/or (c) comprises a nucleotide sequence consisting of SEQ ID NO: 12, and/or wherein the second amplification oligomer of (e), (f), (g), and/or (h) comprises a nucleotide sequence consisting of SEQ ID NO: 12.

18 . The method of claim 16 , wherein the detectable label is an acridinium ester compound.

19 . The method of claim 16 , wherein the amplification reaction at step (2) is an isothermal amplification reaction.

20 . The method of claim 19 , wherein the isothermal amplification reaction is a transcription-mediated amplification (TMA) reaction.